# Molecular dissection of extrachromosomal DNA formation, development, and evolution

> **NIH NIH K99** · STANFORD UNIVERSITY · 2023 · $126,358

## Abstract

PROJECT SUMMARY / ABSTRACT
The devastation wrought by cancer derives primarily from the capacity of tumor cells to evolve. Metastasis,
immune evasion, treatment resistance, and even tumorigenesis itself are evolutionary processes. Our
understanding of tumor evolution is incomplete, evidenced by the ability of some cancers to evolve more
quickly in response to treatment than is compatible with classical genetics. A more comprehensive molecular
understanding of how tumors evolve is key to improving cancer treatment.
 Recent work has shown that oncogene amplification on extrachromosomal DNAs (ecDNAs) is a major
driver of tumor evolution, treatment resistance, and poor outcomes in patients. These circular DNAs are
acentric and have long been thought to asymmetrically segregate at cell division, leading to intratumoral
heterogeneity. We have recently proved this to be the case, but our understanding of the precise mechanisms
through which ecDNA drives tumor evolution remains limited. In this project, Dr. John Rose aims to advance
our understanding of ecDNAs in cancer evolution through unprecedented, well-controlled experimental studies
of ecDNA. First, through a novel approach to image every ecDNA in living cells, I will delineate ecDNA
dynamics on the level of single cells and single ecDNAs (Aim 1a), before extending these findings to organoid
models and analysis of ecDNA+ patient samples (Aim 1b). Second, I will identify the genes that impact ecDNA,
either promoting or inhibiting their accrual in tumor cells, using a high-throughput CRISPR screening strategy
(Aim 2). Finally, I will characterize the development of ecDNAs’ uniquely accessible chromatin structure,
elucidating its etiology (Aim 3). Together, these studies will dramatically improve our understanding of ecDNA
in tumor evolution, while identifying putative avenues for therapeutic intervention.
 This work will be performed in the world-class training environment at Stanford University, under the
mentorship of Dr. Howard Chang, an expert in the application of epigenomics to the study of cancer, and Dr.
Paul Mischel, an expert in extrachromosomal DNA. An advisory committee composed of leaders in the fields of
tumor evolution, computational biology, advanced cell imaging, high-throughput CRISPR screens, and cancer
organoid models will provide additional expertise and mentorship. The first half of each aim will be completed
predominantly during the K99 phase of the award, providing a platform for completion of the aims in the R00
phase.

## Key facts

- **NIH application ID:** 10640520
- **Project number:** 1K99CA279512-01
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** John Christopher Rose
- **Activity code:** K99 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $126,358
- **Award type:** 1
- **Project period:** 2023-08-03 → 2025-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10640520

## Citation

> US National Institutes of Health, RePORTER application 10640520, Molecular dissection of extrachromosomal DNA formation, development, and evolution (1K99CA279512-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10640520. Licensed CC0.

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